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Genomic insights into the spread and evolution of insecticide resistance variants in Anopheles gambiae s.l. from Burkina Faso
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  • Published: 01 April 2026

Genomic insights into the spread and evolution of insecticide resistance variants in Anopheles gambiae s.l. from Burkina Faso

  • Mahamadi Kientega1,
  • Honorine Kaboré1,3,
  • Grégoire Sawadogo1,3,
  • Tin-Yu Y. J. Hui4,
  • Nouhoun Traoré1,
  • Abdoul-Azize A. Millogo1,
  • Hamidou Maiga1,
  • Alistair Miles2,
  • Chris S. Clarkson2 &
  • …
  • Abdoulaye Diabaté1 

Scientific Reports , Article number:  (2026) Cite this article

We are providing an unedited version of this manuscript to give early access to its findings. Before final publication, the manuscript will undergo further editing. Please note there may be errors present which affect the content, and all legal disclaimers apply.

Subjects

  • Evolution
  • Genetics
  • Molecular biology

Abstract

The intensive use of insecticide-based control tools has led to the rapid evolution of resistant phenotypes in malaria vector populations. Understanding the evolutionary processes underlying these resistances is essential to inform the development and deployment of effective control interventions. This study investigated the geographical spread and the genetic background of insecticide resistance variants in Anopheles gambiae s.l. in Burkina Faso. The study identified five pyrethroid-resistant mutations (995F, 995S, 402L(g > t,c), 1527T and 1570Y) at high frequencies. Six diplotype groups were identified, including novel combinations of the resistance-associated alleles (995F, 402L(g > t,c) and 1527T), which formed new genotypes within An. coluzzii populations. These results suggest the emergence of new resistance genotypes in An. coluzzii that are not associated with 995F, probably due to recombination and gene flow events. Interestingly, strong linkage disequilibrium (r2 = 0.821) was observed between 1527T and 402L(g > t) compared to 1527T and 402L(g > c). The PCA revealed three clusters of An. coluzzii populations, driven by 995F, 402L(g > t,c) and 1527T. Other insecticide resistance associated variants such as copy number variations and SNPs in the Ace1 gene (ace1-G280S), cytochrome P450s, esterases and glutathione S-transferases were identified at high frequencies in the same mosquito populations, indicating the intensity and diversity of resistance mechanisms in the country. The study underscores the extent and spreads of insecticide resistance variants in Burkina Faso. It highlights the importance of genomic surveillance of malaria vectors to monitor and detect new resistance variants and to understand the evolutionary processes in vector populations.

Data availability

Jupyter Notebooks and scripts to reproduce all the analyses, tables and figures are available in the GitHub repository: [https://github.com/mkient/AgamBF-IR-2022.git](https:/github.com/mkient/AgamBF-IR-2022.git) . The SNPs and haplotypes data are available on the homepage of MalariaGEN and can be accessed using the malariagen_data package. The raw sequences in FASTQ format and the aligned sequences in BAM format were stored in the European Nucleotide Archive (ENA, Study Accession n° ERR12776294-ERR12871281).

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Acknowledgements

The authors would like to acknowledge the international collaboration, funded by the Wellcome Trust [224487/Z/21/Z], which is working to ensure the safe and sustainable implementation of gene drive technology for malaria vector control in Africa. We would also like to acknowledge the Institut de Recherche en Sciences de la Santé and the Ministry of Health for the implementation of the nationwide sampling of malaria mosquitoes; Institut de Recherche en Sciences de la Santé: Abdoulaye Diabaté, Mahamadi Kientega, Abdoul-Azize Millogo, Lea Pare Toe, Charles Guissou, Hamidou Maïga, Abdoulaye Niang, Simon P. Sawadogo, Nouhoun Traoré, Guel Zila Hyacinthe, Seni Ilboudo, Ali Ouari, Inoussa Toe, Odette Zongo, Gilles Yemien, Gregoire Sawadogo, Honorine Kabore, Achaz Agoulinou, Emmanuel Kiendrebeogo, Sylvie Yerbanga, Soulama Abdoulaye; Ministry of Health of Burkina Faso: the Permanent Secretary for Malaria Elimination (SP-Palu), the community health workers; Imperial college London: Austin Burt, Tin-Yu J. Hui; The authors are also grateful to the MalariaGEN Vector Observatory which is an international collaboration working to build capacity for malaria vector genomic research and surveillance and involves contributions by the following institutions and teams. Wellcome Sanger Institute: Lee Hart, Kelly Bennett, Anastasia Hernandez-Koutoucheva, Jon Brenas, Menelaos Ioannidis, Chris Clarkson, Alistair Miles, Julia Jeans, Paballo Chauke, Victoria Simpson, Eleanor Drury, Osama Mayet, Sónia Gonçalves, Katherine Figueroa, Tom Madison, Kevin Howe, Mara Lawniczak; Liverpool School of Tropical Medicine: Eric Lucas, Sanjay Nagi, Martin Donnelly; Broad Institute of Harvard and MIT: Jessica Way, George Grant; The authors would like to thank the staff of the Wellcome Sanger Genomic Surveillance unit and the Wellcome Sanger Institute Sample Logistics, Sequencing and Informatics facilities for their contributions. The MalariaGEN Vector Observatory is supported by funding awarded to Dominic Kwiatkowski and Mara Lawniczak from Wellcome (220540/Z/20/A, ‘Wellcome Sanger Institute Quinquennial Review 2021-2026’) and funding awarded to Dominic Kwiatkowski from the Bill and Melinda Gates Foundation (INV-001927). The Liverpool School of Tropical Medicine’s participation was supported by the National Institute of Allergy and Infectious Diseases ([NIAID] R01-AI116811), with additional support from the Medical Research Council (MR/P02520X/1). The latter grant is a UK-funded award and is part of the EDCTP2 programme supported by the European Union. Martin Donnelly is supported by a Royal Society Wolfson Fellowship (RSWF\FT\180003). The Pan-African Mosquito Control Association’s participation was funded by the Bill and Melinda Gates Foundation (INV-031595). The authors would also like to thank the health workers and the populations of the sampling sites for their sincere cooperation during the mosquito sample collection.

Funding

The mosquito sampling and data analyses are supported by the Institut de Recherche en Sciences de la Santé, which received core funding from the Bill & Melinda Gates Foundation [INV-037164] and the Wellcome trust [224487/Z/21/Z]. The MalariaGEN Vector Observatory is supported by multiple institutes and funders. The Wellcome Sanger Institute’s participation was supported by funding from Wellcome (220540/Z/20/A, ‘Wellcome Sanger Institute Quinquennial Review 2021–2026’) and the Bill & Melinda Gates Foundation (INV-001927 and INV-068808).

Author information

Authors and Affiliations

  1. Institut de Recherche en Sciences de la Santé (IRSS), 01 BP 545, Bobo- Dioulasso, Burkina Faso

    Mahamadi Kientega, Honorine Kaboré, Grégoire Sawadogo, Nouhoun Traoré, Abdoul-Azize A. Millogo, Hamidou Maiga & Abdoulaye Diabaté

  2. Vector Surveillance Programme, Genomic Surveillance Unit, Wellcome Sanger Institute, Hinxton, Cambridge, UK

    Alistair Miles & Chris S. Clarkson

  3. Université Nazi Boni, 01 BP 1091, Bobo-Dioulasso, Burkina Faso

    Honorine Kaboré & Grégoire Sawadogo

  4. Department of Life Sciences, Imperial College London, Silwood Park, Ascot, SL5 7PY, UK

    Tin-Yu Y. J. Hui

Authors
  1. Mahamadi Kientega
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  2. Honorine Kaboré
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Contributions

MK and HK conceived the study. AD and AM provided funding and resources. AD, HM and CSC supervised the study. MK, HM, AAM, NT, GS and HK carried out samples collection in the field. AM and CSC produced the genomic data. MK, HTY and HK carried out data analysis and visualization. MK and HK drafted the manuscript. All authors have read and approved this version of the manuscript.

Corresponding authors

Correspondence to Mahamadi Kientega or Abdoulaye Diabaté.

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The authors declare no competing interests.

Ethical approval

All methods in this paper have been implemented in accordance with the relevant guidelines/regulations/legislation in Burkina Faso. The protocol of the sampling was approved by the Institutional Ethics Committee of the Institut de Recherche en Sciences de la Santé (32-2022/CEIRES). No ethics approval was required to run all the activities related to this paper.

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Supplementary Information

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41598_2026_45950_MOESM1_ESM.xlsx (download XLSX )

Fig. S1. Heat map showing the CNVs frequencies of the carboxylesterase genes in the An. gambiae s.l. populations of Burkina Faso. The X axis shows the An. gambiae s.l. populations and the sampling sites. The Y axis shows the positions of the carboxylesterase genes in the genomes and the CNV type (amp: gene amplification, del: gene deletion). The gradient color bar shows the distribution of the allelic frequencies. Bana: Bana Village, Side: Sideradougou, Sour: Souroukoudinga, Po-D: Po-Dongo, Nass: Nassan, Naga: Nagaré, Ouro: Ouro-Hesso, Degu: Deguê-Deguê.

41598_2026_45950_MOESM2_ESM.xlsx (download XLSX )

Fig. S2. Heat map showing the CNVs frequencies of the glutathione-s-transferase genes in the An. gambiae s.l. populations of Burkina Faso. The X axis shows the An. gambiae s.l. populations and the sampling locations. The Y axis shows the positions of the glutathione‑s‑transferase genes in the genomes and the CNV type (amp: gene amplification, del: gene deletion). The gradient color bar shows the distribution of the allelic frequencies. Bana: Bana Village, Side: Sideradougou, Sour: Souroukoudinga, Po-D: Po-Dongo, Nass: Nassan, Naga: Nagaré, Ouro: Ouro-Hesso, Degu: Deguê-Deguê.

41598_2026_45950_MOESM3_ESM.xlsx (download XLSX )

Fig. S3. Heat map showing the CNVs frequencies of the cytochrome P450 genes in the An. gambiae s.l. populations of Burkina Faso. The X axis shows the An. gambiae s.l. populations and the sampling locations. The Y axis shows the positions of the cytochrome p450 genes in the genomes and the CNV type (amp: gene amplification, del: gene deletion). The gradient color bar shows the distribution of the allelic frequencies. Bana: Bana Village, Side: Sideradougou, Sour: Souroukoudinga, Po-D: Po-Dongo, Nass: Nassan, Naga: Nagaré, Ouro: Ouro-Hesso, Degu: Deguê-Deguê.

41598_2026_45950_MOESM4_ESM.xlsx (download XLSX )

Table S1. Distribution of the non-synonymous SNPs frequencies of the VGSC gene (2L: 2358158 - 2431617) within An. gambiae s.l. populations in 8 sites in Burkina Faso.

Table S2. Genotype frequencies of the kdr diplotypes in Burkina Faso. (download PNG )

41598_2026_45950_MOESM6_ESM.png (download PNG )

Table S3. Distribution of the non-synonymous SNPs frequencies of the ACE1 gene (2R: 3484107 - 3495790) within An. gambiae s.l. populations in 8 sites in Burkina Faso.

41598_2026_45950_MOESM7_ESM.png (download PNG )

Table S4. Distribution and position of the copy number variation identified in the Anopheles gambiae populations in Burkina Faso.

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Kientega, M., Kaboré, H., Sawadogo, G. et al. Genomic insights into the spread and evolution of insecticide resistance variants in Anopheles gambiae s.l. from Burkina Faso. Sci Rep (2026). https://doi.org/10.1038/s41598-026-45950-y

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  • Received: 21 November 2025

  • Accepted: 23 March 2026

  • Published: 01 April 2026

  • DOI: https://doi.org/10.1038/s41598-026-45950-y

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Keywords

  • Insecticide
  • Resistance
  • Genomics
  • An. gambiae s.l.
  • Malaria
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